Skip to main content
SpringerLink
Log in

Analysis of DNA Methylation in Pancreatic Cancer: An Update

  • Protocol
  • First Online:
Cancer Epigenetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1238))

Abstract

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive tumor and the fourth common cause of cancer death in the Western world. The lack of effective therapeutic strategies is due to the late diagnosis of this disease. Methylation markers could improve early detection and help in the surveillance of PDAC after treatment. Analysis of hypermethylation in the tumor tissue might help to identify new therapeutic strategies and aid in the understanding of the pathophysiological changes occurring in pancreatic cancer. There are several methods for the detection of methylated events, but methylation-specific PCR (MSP-PCR) is the method of choice if a small number of genes will be tested in a larger set of patients samples. After isolation of the DNA by standard procedure, the DNA is then modified using sodium bisulfide.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Siegel R, Naishadham D, Jemal A (2013) Cancer statistics, 2013. CA Cancer J Clin 63:11–30

    Article  PubMed  Google Scholar 

  2. Schneider G, Siveke JT, Eckel F, Schmid RM (2005) Pancreatic cancer: basic and clinical aspects. Gastroenterology 128:1606–1625

    Article  CAS  PubMed  Google Scholar 

  3. Kulis M, Esteller M (2010) DNA methylation and cancer. Adv Genet 70:27–56

    Article  PubMed  Google Scholar 

  4. Nakhasi HL, Lynch KR, Dolan KP, Unterman RD, Feigelson P (1981) Covalent modification and repressed transcription of a gene in hepatoma cells. Proc Natl Acad Sci U S A 78:834–837

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  5. Wissmann C, Wild PJ, Kaiser S, Roepcke S, Stoehr R, Woenckhaus M, Kristiansen G, Hsieh J-C, Hofstaedter F, Hartmann A, Knuechel R, Rosenthal A, Pilarsky C (2003) WIF1, a component of the Wnt pathway, is down-regulated in prostate, breast, lung, and bladder cancer. J Pathol 201:204–212

    Article  CAS  PubMed  Google Scholar 

  6. Dutruel C, Bergmann F, Rooman I, Zucknick M, Weichenhan D, Geiselhart L, Kaffenberger T, Rachakonda PS, Bauer A, Giese N, Hong C, Xie H, Costello JF, Hoheisel J, Kumar R, Rehli M, Schirmacher P, Werner J, Plass C, Popanda O, Schmezer P (2014) Early epigenetic downregulation of WNK2 kinase during pancreatic ductal adenocarcinoma development. Oncogene 33(26):3401–3410

    Article  CAS  PubMed  Google Scholar 

  7. Sato N, Fukushima N, Hruban RH, Goggins M (2008) CpG island methylation profile of pancreatic intraepithelial neoplasia. Mod Pathol 21:238–244

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  8. Lofton-Day C, Model F, Devos T, Tetzner R, Distler J, Schuster M, Song X, Lesche R, Liebenberg V, Ebert M, Molnar B, Grützmann R, Pilarsky C, Sledziewski A (2008) DNA methylation biomarkers for blood-based colorectal cancer screening. Clin Chem 54:414–423

    Article  CAS  PubMed  Google Scholar 

  9. Tan AC, Jimeno A, Lin SH, Wheelhouse J, Chan F, Solomon A, Rajeshkumar NV, Rubio-Viqueira B, Hidalgo M (2009) Characterizing DNA methylation patterns in pancreatic cancer genome. Mol Oncol 3:425–438

    Article  CAS  PubMed  Google Scholar 

  10. Murphy PJ, Cipriany BR, Wallin CB, Ju CY, Szeto K, Hagarman JA, Benitez JJ, Craighead HG, Soloway PD (2013) Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells. Proc Natl Acad Sci U S A 110:7772–7777

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  11. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462:315–322

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  12. Stirzaker C, Taberlay PC, Statham AL, Clark SJ (2014) Mining cancer methylomes: prospects and challenges. Trends Genet 30(2):75–84

    Article  CAS  PubMed  Google Scholar 

  13. Slieker RC, Bos SD, Goeman JJ, Bovée JV, Talens RP, van der Breggen R, Suchiman HED, Lameijer E-W, Putter H, van den Akker EB, Zhang Y, Jukema JW, Slagboom PE, Meulenbelt I, Heijmans BT (2013) Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array. Epigenetics Chromatin 6:26

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  14. Sánchez-Vega F, Gotea V, Petrykowska HM, Margolin G, Krivak TC, Deloia JA, Bell DW, Elnitski L (2013) Recurrent patterns of DNA methylation in the ZNF154, CASP8, and VHL promoters across a wide spectrum of human solid epithelial tumors and cancer cell lines. Epigenetics 8:1355–1372

    Article  PubMed Central  PubMed  Google Scholar 

  15. Morris TJ, Butcher LM, Feber A, Teschendorff AE, Chakravarthy AR, Wojdacz TK, Beck S (2014) ChAMP: 450k chip analysis methylation pipeline. Bioinformatics 30(3):428–430

    Article  CAS  PubMed  Google Scholar 

  16. Wehrum D, Grützmann R, Hennig M, Saeger H-D, Pilarsky C (2008) Recent patents concerning diagnostic and therapeutic applications of aberrantly methylated sequences in pancreatic cancer. Recent Pat DNA Gene Seq 2:97–106

    Article  CAS  PubMed  Google Scholar 

  17. Thun M, Jemal A, Desantis C, Blackard B, Ward E (2009) An overview of the cancer burden for primary care physicians. Prim Care 36:439–454

    Article  PubMed  Google Scholar 

  18. Kuroki T, Yendamuri S, Trapasso F, Matsuyama A, Aqeilan RI, Alder H, Rattan S, Cesari R, Nolli ML, Williams NN, Mori M, Kanematsu T, Croce CM (2004) The tumor suppressor gene WWOX at FRA16D is involved in pancreatic carcinogenesis. Clin Cancer Res 10:2459–2465

    Article  CAS  PubMed  Google Scholar 

  19. Zhao G, Qin Q, Zhang J, Liu Y, Deng S, Liu L, Wang B, Tian K, Wang C (2013) Hypermethylation of HIC1 promoter and aberrant expression of HIC1/SIRT1 might contribute to the carcinogenesis of pancreatic cancer. Ann Surg Oncol 20(Suppl 3):301–311

    Article  Google Scholar 

  20. Yao F, Sun M, Dong M, Jing F, Chen B, Xu H, Wang S (2013) NPTX2 hypermethylation in pure pancreatic juice predicts pancreatic neoplasms. Am J Med Sci 346:175–180

    Article  PubMed  Google Scholar 

  21. Yang L, Yang H, Li J, Hao J, Qian J (2013) ppENK gene methylation status in the development of pancreatic carcinoma. Gastroenterol Res Pract 2013:130927

    PubMed Central  PubMed  Google Scholar 

  22. Yamamura A, Miura K, Karasawa H, Morishita K, Abe K, Mizuguchi Y, Saiki Y, Fukushige S, Kaneko N, Sase T, Nagase H, Sunamura M, Motoi F, Egawa S, Shibata C, Unno M, Sasaki I, Horii A (2013) Suppressed expression of NDRG2 correlates with poor prognosis in pancreatic cancer. Biochem Biophys Res Commun 441:102–107

    Article  CAS  PubMed  Google Scholar 

  23. Wang P, Chen L, Zhang J, Chen H, Fan J, Wang K, Luo J, Chen Z, Meng Z, Liu L (2014) Methylation-mediated silencing of the miR-124 genes facilitates pancreatic cancer progression and metastasis by targeting Rac1. Oncogene 33(4):514–24

    Article  CAS  PubMed  Google Scholar 

  24. Thu KL, Radulovich N, Becker-Santos DD, Pikor LA, Pusic A, Lockwood WW, Lam WL, Tsao MS (2014) SOX15 is a candidate tumor suppressor in pancreatic cancer with a potential role in Wnt/β-catenin signaling. Oncogene 33(3):279–288

    Google Scholar 

  25. Park JS, Park YN, Lee KY, Kim JK, Yoon DS (2013) P16 hypermethylation predicts surgical outcome following curative resection of mid/distal bile duct cancer. Ann Surg Oncol 20:2511–2517

    Article  PubMed  Google Scholar 

  26. Zhao L, Cui Q, Lu Z, Chen J (2012) Aberrant methylation of RASSF2A in human pancreatic ductal adenocarcinoma and its relation to clinicopathologic features. Pancreas 41:206–211

    Article  CAS  PubMed  Google Scholar 

  27. Zhang L, Gao J, Li Z, Gong Y (2012) Neuronal pentraxin II (NPTX2) is frequently down-regulated by promoter hypermethylation in pancreatic cancers. Dig Dis Sci 57:2608–2614

    Article  CAS  PubMed  Google Scholar 

  28. Wu Y, Li J, Sun CY, Zhou Y, Zhao YF, Zhang SJ (2012) Epigenetic inactivation of the canonical Wnt antagonist secreted frizzled-related protein 1 in hepatocellular carcinoma cells. Neoplasma 59:326–332

    Article  CAS  PubMed  Google Scholar 

  29. Li M, Zhao ZW (2012) Clinical implications of mismatched repair gene promoter methylation in pancreatic cancer. Med Oncol 29:970–976

    Article  CAS  PubMed  Google Scholar 

  30. Hong S-M, Omura N, Vincent A, Li A, Knight S, Yu J, Hruban RH, Goggins M (2012) Genome-wide CpG island profiling of intraductal papillary mucinous neoplasms of the pancreas. Clin Cancer Res 18:700–712

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  31. Heichman KA, Warren JD (2012) DNA methylation biomarkers and their utility for solid cancer diagnostics. Clin Chem Lab Med 50:1707–1721

    Article  CAS  PubMed  Google Scholar 

  32. Giovannetti E, Erozenci A, Smit J, Danesi R, Peters GJ (2012) Molecular mechanisms underlying the role of microRNAs (miRNAs) in anticancer drug resistance and implications for clinical practice. Crit Rev Oncol Hematol 81:103–122

    Article  PubMed  Google Scholar 

  33. Park JK, Ryu JK, Yoon WJ, Lee SH, Lee GY, Jeong K-S, Kim Y-T, Yoon YB (2012) The role of quantitative NPTX2 hypermethylation as a novel serum diagnostic marker in pancreatic cancer. Pancreas 41:95–101

    Article  CAS  PubMed  Google Scholar 

  34. Biewusch K, Heyne M, Grutzmann R, Pilarsky C (2012) DNA methylation in pancreatic cancer: protocols for the isolation of DNA and bisulfite modification. Methods Mol Biol 863:273–280

    Article  CAS  PubMed  Google Scholar 

  35. Wright DK, Manos MM (1990) Sample preparation from paraffin-embedded tissues. In: Innis MA, Gelfont DH, Sninsky JJ, White TJ (eds) PCR protocols: a guide to methods and applications. Academic, San Diego, pp 153–158

    Chapter  Google Scholar 

Download references

Acknowledgements

We are grateful to Beatrix Jahnke for performing DNA isolation and bisulfite modification in my lab. Thanks also to Alfred E. Neumann for fruitful discussions.

Author information

Authors and Affiliations

  1. Department of Surgery, Medizinische Fakultät Carl Gustav Carus, TU Dresden, Fetscherstr. 74, 01307, Dresden, Germany

    Christian Pilarsky Ph.D. & Robert Grützmann

Authors
  1. Christian Pilarsky Ph.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Robert Grützmann
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Christian Pilarsky Ph.D. .

Editor information

Editors and Affiliations

  1. National Institutes of Health, Rockville, Maryland, USA

    Mukesh Verma

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer Science+Business Media New York

About this protocol

Cite this protocol

Pilarsky, C., Grützmann, R. (2015). Analysis of DNA Methylation in Pancreatic Cancer: An Update. In: Verma, M. (eds) Cancer Epigenetics. Methods in Molecular Biology, vol 1238. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1804-1_9

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-1804-1_9

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-1803-4

  • Online ISBN: 978-1-4939-1804-1

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation